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Shaoxing rice wine is a notable exemplar of Chinese rice wine. Its superior quality is strongly correlated with the indigenous natural environment. The results indicated that Firmicutes (75%), Actinobacteria (15%), Proteobacteria (5%), and Bacteroidetes (3%) comprised the prevailing bacterial groups. Among the main bacterial genera, <i>Lactobacillus</i> was the most abundant, accounting for 49.4%, followed by <i>Lactococcus</i> (11.9%), <i>Saccharopolyspora</i> (13.1%), <i>Leuconostoc</i> (4.1%), and <i>Thermoactinomyces</i> (1.1%). The dominant fungal phyla were Ascomycota and Zygomycota. Among the dominant genera, <i>Saccharomyces</i> (59.3%) prevailed as the most abundant, followed by <i>Saccharomycopsis</i> (10.7%), <i>Aspergillus</i> (7.1%), <i>Thermomyces</i> (6.2%), <i>Rhizopus</i> (4.9%), <i>Rhizomucor</i> (2.2%), and <i>Mucor</i> (1.3%). The findings demonstrate that the structure of the bacterial and fungal communities remains stable in the environment, with their diversity strongly influenced by climatic conditions. The continuous fluctuations in environmental factors, such as temperature, air pressure, humidity, rainfall, and light, significantly impact the composition and diversity of microbial populations, particularly the dominant bacterial community.